Hi,
Was impressed by the Worflow screencasts but when I converted my
history
to a workflow it failed. This is because some of the tools output
tabular data, but some downstream tools require interval format input
and therefore fail. When I made the history I manually changed the
file
format and nominated the fields for chr,start,end,strand, but this is
lost in the workflow. Obvious ideas:
* Use a tabular-to-interval tool - I looked but can't find one
* Only used tools which output interval format - a less desirable
solution. e.g. I can't figure out how to filter out duplicate codons
in
my gene-BED-to-codon-BED file except using the statistics->count
function which outputs tabular.
Has anyone worked out how to change formats within a workflow?
regards,
Paul

Paul,
We're working on a new feature that'll allow extra actions within
workflows that should cover this case, and it will be available soon.
Regarding a workaround for this specific scenario, would you mind
sharing the workflow with 'dannon.baker@emory.edu' ? That way I can
take a look and see if I can come up with something that'll work for
you in the short term, as well as verifying that the new workflow
actions will handle the task.
Thanks for using Galaxy,
-Dannon

Dannon,
Thanks for your interest. It would be a handy feature to be able to
attach metadata to tabular files in the workflow. I have shared the
workflow. It is called 'chr21 analysis'. Input is a gene BED file for
a
chromosome region from UCSC data (which includes gene variants).
Workflow fails after I use "count" to get only unique records from my
codon file. The other input is a list of SNPs in the same region.
regards,
Paul